<html>
<head>
<link rel="stylesheet" type="text/css" href="css/dasBrowser.css" />
<script type="text/javascript" src="js/jquery-1.4.2.js" ></script>
<script type="text/javascript" src="extJs/sessvars/sessvars.js" ></script>
<script type="text/javascript" src="js/genunz.js" ></script>




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<!--CSS file (default YUI Sam Skin) -->
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<link rel="stylesheet" type="text/css" href="css/dasBrowser.css">



<!-- Dependencies -->
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<script>
//sessvars.$.debug();
YAHOO.namespace("dasRegistry");
sessvars.karyoDas = new Object();
sessvars.karyoDas.conf = new Object();
sessvars.karyoDas.conf.sources = new Array();
sessvars.karyoDas.conf.userEntryPoints = [];
sessvars.karyoDas.conf.zoomConf = [];
sessvars.karyoDas.conf.userContainers = [];
sessvars.karyoDas.conf.specie = new String();
</script>

<script type="text/javascript" src="intJs/viewer/init.js"></script>
<script type="text/javascript" src="intJs/viewer/drawKaryotypeStructure.js"></script>
<script type="text/javascript" src="intJs/viewer/classes.js"></script>
<script type="text/javascript" src="intJs/viewer/dasParsers.js"></script>
<script type="text/javascript" src="intJs/search/searchDataTables.js"></script>
<script type="text/javascript" src="intJs/search/searchRequests.js"></script>
<script type="text/javascript" src="intJs/viewer/util.js"></script>
<script type="text/javascript" src="intJs/viewer/karyotypeStructureFunctions.js"></script>


<script>

YAHOO.startSelectedSources = function(){
	YAHOO.dasRegistry.setContainers("karyoDas",{KDsources:"DAS Sources"});
	YAHOO.dasBrowser.genome.panel.setPanelListeners("KDsources", true);
	YAHOO.dasBrowser.genome.panel.setPanelTitleStyle("KDsources");
	YAHOO.dasRegistry.sourcesControl = {numberOfRequests:0,successCount:0};

    YAHOO.dasRegistry.listOfSources = new Array();

    //HGNC
    var source = new Object();
    source.url ='http://das.sanger.ac.uk/das/hgnc36/features';
    source.title ='Gene Names';
    source.description ='Ensembl HGNC genes, NCBI36 assembly';
    source.ntLimit =17000000;
    YAHOO.dasRegistry.listOfSources.push(source);

    /*
    var source = new Object();
    source.url ='http://mykaryoview.com:9000/das/mykaryoview/features';
    source.title ='23andMe Dummy';
    source.description ='SNPs taken from 23andMe';
    source.ntLimit =17000000;
    YAHOO.dasRegistry.listOfSources.push(source);
  */
  
  //Redon
  var source = new Object();
  source.url ='http://das.sanger.ac.uk/das/WGTP_loci_36/features';
  source.title ='Redon Clones';
  source.description ='CNVs reported in normal individuals';
  source.ntLimit =10000;
  YAHOO.dasRegistry.listOfSources.push(source);
  
  var source = new Object();
  source.url ='http://das.sanger.ac.uk/das/toronto_poly_36/features';
  source.title ='Database of Genomic Variants';
  source.description ='Normal, Autism and Cancer Variation from literature';
  source.ntLimit =10000;
  source.stylesheet = true;
  YAHOO.dasRegistry.listOfSources.push(source);
  
  
    //COSMIC
  var source = new Object();
  source.url ='http://das.sanger.ac.uk/das/cosmic_transcripts_ncbi36/features';
  source.title ='COSMIC';
  source.description ='Somatic Mutations in Human Cancer';
  source.ntLimit =10000;
  source.stylesheet = true;
  YAHOO.dasRegistry.listOfSources.push(source);
  
  //OMIM 
  var source = new Object();
  source.url ='http://das.sanger.ac.uk/das/ens_36_omim_genes/features';
  source.title ='OMIM';
  source.description ='Catalogue of Human Genes Involved in Mendelian Genetic Disorders';
  source.ntLimit =10000;
  source.stylesheet = true;
  YAHOO.dasRegistry.listOfSources.push(source);
  
  
    
	
	YAHOO.dasRegistry.displayDataTable();
}


/**
 * General configuration
 */

sessvars.karyoDas.conf.selectedDsnId = "Homo_sapiens.GRCh37.reference";
sessvars.karyoDas.conf.userEntryPoints = [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,'X','Y'];
//sessvars.karyoDas.conf.userEntryPoints = [1];
sessvars.karyoDas.conf.zoomConf = [];
sessvars.karyoDas.conf.userContainers = ['zoomView', 'chromosomeView', 'karyotypeView'];
YAHOO.util.Event.addListener(window, 'load', YAHOO.startSelectedSources);

</script>


<link rel="stylesheet" type="text/css" href="extJs/build/fonts/fonts-min.css" />


</head>
<body class="yui-skin-sam">
 <div style="padding:25px;">
  <!-- left panel -->
  <div style="float:left">
<table border="0px">
    <tr><td style="border:0px;width:50px"><a href="index.html" ><img src="myKaryoView-small.png"></img></a></td></tr>
    <tr><td style="border:0px;text-align:center"><h1>myKaryoView </h1><h3>Personalized Genome Search</h3></td></tr>
<tr><td><a href="about.html">About</a></td></tr>
    <tr><td><a href="http://mykaryoview.com/mykaryoview_doc.pdf">Documentation</a></td></tr>
    <tr><td><a href="http://mykaryoview.com/client.zip">Download</a></td></tr>
    <tr><td><a href="acknowledgements.html">Acknowledgements</a></td></tr>
    <tr><td><a href="disclaimer.html">Disclaimer</a></td></tr>
  </table>     
  </div>
  <form id="target" action="display.html" method="post">
  
  <!-- Source selector -->
  <div style="float:left;padding:25px">
  
     <h1>1. Select sources</h1>
     <div id="karyoDas"></div>    
  </div>
  
  <!-- left panel -->
  <div style="width:900px">
  <div style="float:left;margin-left:30px;margin-top:10px">  
  <div class="markup">
    <h1 style="margin-bottom:20px">2. Input your personal data source (optional)</h1>
       <input type="text" id="usersource" value="">
       &nbsp&nbsp&nbsp<b><i>How do I do that?</i></b>
       <br/>
       <p>e.g. http://www.ebi.ac.uk/das-srv/easydas/bernat/das/full_genome</p>
  </div></div>
  <!-- box 2 -->
  <div style="float:left;margin-left:30px"> 
     <h1>3. Enter gene name* or coordinates and submit</h1>
     <input size="30" autocomplete="off" type="text" id="inputString" >
     <input type="submit" id="viewButton" name="submit"/>
     
     <p>e.g. 8:5900000,6000000</p>
     <div class="suggestionsBox" id="suggestions" style="display: none;">
       <img src="img/upArrow.png" style="position: relative; top: -12px; left: 30px" alt="upArrow" />
       <div class="suggestionList" id="autoSuggestionsList"></div>
     </div>
     <p style="color: red; font-size:10px;">*Select gene names from the drop-down menu.</p>
   </div>
  </form>
  </div>
  
 </div>
</body>
</html>
